[Bio] / FigMetagenomeTools / separatemultifasta.pl Repository:
ViewVC logotype

View of /FigMetagenomeTools/separatemultifasta.pl

Parent Directory Parent Directory | Revision Log Revision Log

Revision - (download) (as text) (annotate) (vendor branch)
Mon Feb 19 17:15:26 2007 UTC (13 years, 3 months ago) by olson
Branch: x, MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, mgrast_rel_2008_0806, mgrast_dev_10262011, mgrast_dev_02212011, mgrast_rel_2008_0923, mgrast_release_3_0, mgrast_dev_03252011, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, mgrast_rel_2008_0919, mgrast_rel_2008_1110, myrast_33, mgrast_rel_2008_0917, mgrast_dev_04052011, mgrast_dev_02222011, y, HEAD
Changes since 1.1: +0 -0 lines
Initial import

#!/usr/bin/perl -w

# rewritten with BioPerl

use strict;
use Bio::SeqIO;

my $file=shift || die "$0 <fasta file>";
my $dir=$file.".files";
if (-e $dir) {die "$dir already exists. Not overwriting"}
else {mkdir $dir, 0755}

my %seen;
my $sio=Bio::SeqIO->new(-file=>$file, -format=>"fasta");
while (my $seq=$sio->next_seq)
 my $id=$seq->id;
 $id =~ s/\s+/_/g;
 while ($seen{$id}) {print "$id already written, "; $id.="1"; print " now trying $id\n"}
 my $fout=Bio::SeqIO->new(-file=>">$dir/$id.fasta", -format=>"fasta");

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3